Research workbench
Open state of RAD24-RFC:9-1-1 bound to a 5' SS/DSDNA junction
Analyse Open state of RAD24-RFC:9-1-1 bound to a 5' SS/DSDNA junction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DQW
- Type
- protein + DNA
- Length
- 2,837 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replication factor C subunit 4; Replication factor C subunit 3; Replication factor C…
- UniProt
- P40339, P38629, P40348, P38251, A0A8H4BW58, A0A8H4BUG7, Q02574, A0A8H8UM36
- Ligands
- AGS, GDP, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 10 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Replication factor C subunit 4 | protein | 315 | 63% helix, 9% strand | P40339 |
| C | Replication factor C subunit 3 | protein | 327 | 62% helix, 9% strand | P38629 |
| D | Replication factor C subunit 2 | protein | 335 | 59% helix, 9% strand | P40348 |
| E | Replication factor C subunit 5 | protein | 354 | 56% helix, 14% strand | P38251 |
| F | DNA damage checkpoint control protein RAD17 | protein | 293 | 24% helix, 43% strand | A0A8H4BW58 |
| G | DDC1 isoform 1 | protein | 340 | 25% helix, 39% strand | A0A8H4BUG7 |
| H | DNA damage checkpoint control protein MEC3 | protein | 316 | 25% helix, 37% strand | Q02574 |
| A | RAD24 isoform 1 | protein | 522 | 54% helix, 6% strand | A0A8H8UM36 |
| J | DNA (50-mer) | dna | 25 | — | — |
| I | DNA (5'-D(P*CP*GP*TP*CP*CP*CP*TP*TP*CP*C)-3') | dna | 10 | — | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains B, C, D, E, A
- GDP · Guanosine-5'-diphosphate · ligand · chains E
- MG · Magnesium ion · metal · 4 copies · chains B, C, D, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.84 | 0.90 | 60 | GDP |
| 2 | 198 | 0.82 | 0.96 | 45 | MG, AGS |
| 3 | 442 | 0.81 | 0.89 | 57 | empty |
| 4 | 167 | 0.81 | 0.97 | 31 | MG, AGS |
| 5 | 609 | 0.81 | 0.86 | 59 | empty |
Interfaces
24 interfaces between chains.
- E–A · 3332 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2813 Ų buried · 41 hydrogen bonds · protein-protein
- B–A · 2689 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2468 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2456 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 8DQW · Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction · the same entry in another collection · chain I against I, TM-score 1.00
- P40348 · AlphaFold monomer V2.0 prediction for replication factor C subunit 2 (P40348) · a predicted model of the same protein · chain D against A, TM-score 0.96
- P38251 · AlphaFold monomer V2.0 prediction for replication factor C subunit 5 (P38251) · a predicted model of the same protein · chain E against A, TM-score 0.94
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P40339
- Every structure of UniProt P38629
- Every structure of UniProt P40348
- Every structure of UniProt P38251
- Every structure of UniProt A0A8H4BW58
- Every structure of UniProt A0A8H4BUG7
- Every structure of UniProt Q02574
- Every structure of UniProt A0A8H8UM36
- Elsewhere: RCSB PDB 8DQW · PDBe 8DQW · UniProt P40339 · UniProt P38629 · UniProt P40348 · UniProt P38251 · UniProt A0A8H4BW58 · UniProt A0A8H4BUG7 · UniProt Q02574 · UniProt A0A8H8UM36
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